My SS came with the polished wheels, and under certain light conditions it looks like they have scratches in them. Are these wheels clear coated and will waxing clear up the scratches, or are they bare aluminum and I need to use polish on them?

YES, they are clear coated.......the best this you can do to keep them as nice as possible, is exactly what you sugested. Wash them, even the back side, and put a good coat of wax on them. that will make it a lot easier to clean them too.